Most grape breeders are aware of this, but it doesn't feel comfortable. That's the socio-political or cultural side intruding on our thoughts.
As breeders, we should try to differentiate the scientific and cultural, though. Vinifera means 'European commercial grape' and European's have every right to define what specific ancestry provide membership in that socio-political class. If Canadians want to think of themselves as 'European', and use the same definition for vinifera, it is equally logical.
Logical, but delightfully inconsistent. Folks in Germany, who have an interest in doing things differently than France, call the variety 'Regent' vinifera. Folks in Canada, who have an interest in doing things like they are done in France, don't. In fact, sales of 'Regent' grapes are banned in Canada.
In general, I try to avoid using the term 'vinifera' entirely. When the term comes to mind, I just replace it with 'European commercial grape'. Everyone knows what I mean, and there is no confusion between the scientific and socio-political. If we want to breed a healthy, good tasting grape for the region we live in, the term 'vinifera' confuses our efforts.
Of course, once you want to sell the results of your breeding, the socio-political is impossible to avoid. Participating in the world of commerce requires one to live with certain logical impossibilities.
Ref: "A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change" Yizhen Wan,et. al.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3750556/